1D 1H NMR data processing  science

1D 1H NMR is a common technique applied to metabolomic studies, being well suited to untargeted analysis of complex biofluids. It has been successfully applied to the classification and diagnosis of a number of diseases including [ref]. There are a number of important steps that must be applied prior ... Continue reading

Gremlins in the Machine: Creating custom tools for the Pathomx data analysis platform  data-science

Pathomx is a workflow-based data analysis tool built on IPython. It began as a metabolomic-analysis toolkit, but has extended to support general data analysis workflows. It aims to be simple to use for non-experts while powerful enough for complex analysis tasks. Key to both of these goals is the ability ... Continue reading

Automatic phase correction of NMR spectra  science

This notebook demonstrates automatic phase correction algorithms implemented for nmrglue. Two standard algorithms are implemented: ACME algorithm by Chen Li et al. Journal of Magnetic Resonance 158 (2002) 164-168 Naive peak minima minimisation The outputs for the two algorithms are shown below. Automatic phase correction can be used through the addition of an autops Continue reading

NMRLab 1D NMR processing (MATLAB)  science

This notebook uses a subset of the available processing features in NMRLab (+Metabolab) to process 1D NMR spectra. The output is saved as a CSV file that can be imported into pandas, PLS_Toolbox or any other package for subsequent analysis. To use this workbook you will need an installation of MATLAB Continue reading

MetaboHunter 1D NMR Identification (Python Interface) Demo  science

MetaboHunter is a web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra. Identification is performed in comparison to two publicly available databases (HMDB, MMCD) of NMR standard measurements. More information about the algorithm is available in the published paper: Tulpan, D., Leger, S., Belliveau, L., Culf, A., Cuperlovic-Culf, M. (2011). MetaboHunter: semi-automatic identification of 1H-NMR metabolite spectra in complex mixtures Continue reading

BioCyc Interface Demo  science

This notebook is a quick demo of a BioCyc Web API I’ve released for Python. While incomplete the API offers access to most basic attributes for metabolites, proteins, reactions, pathways and organisms in the database. The Python interface comes with an disk-based caching mechanism under ~/.biocyc that greatly reduces the delay (and load) for BioCyc servers. Continue reading

Dot Blot Analysis with ImageJ  science

Analyzing a dot blot in ImageJ by background subtraction and measuring the integrated density of each dot. This dot blot image is available in the File/Open Samples menu in ImageJ 1.33s or later. Method This method usually requires background correction of the image, which can be done using ... Continue reading

Measuring cell fluorescence using ImageJ  science

Determining the level of cellular fluorescence from fluorescence microscopy images in ImageJ Open ImageJ. Note: ImageJ may be freely downloaded from [here](http://rsbweb.nih.gov/ij/download.html) Select the cell of interest using any of the drawing/selection tools (i.e. rectangle, circle, polygon or freeform) From the ... Continue reading

Transmit extra data with signals in PyQt  gui

Signals are a neat feature of Qt that allow message-passing between different areas of your program. To use a signal you attach a function to be called in the event of the signal firing, usually accepting a small item of data about the signal state. However, there is a limitation: the signal can only emit the data it was designed to do. So for example, a QAction has a .triggered that fires when that particular action has been activated. Unfortunately the receiving connected function only receives one thing: checked=True or False. In other words, the receiving function has no way of knowing which action triggered it. This is usually fine. You can tie a particular action to a particular function. However, sometimes you want to trigger multiple actions off the same type of action, and treat them differently. Here’s a neat trick to do just that. Continue reading

Pathomx: Example Analysis  science

Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service. The video shows an example analysis from processed data through ... Continue reading

cx_Freeze and PySide on Mac  gui

I’d had success using py2app for building Mac binaries for distribution but wanted to give cx_Freeze a go since it’s cross platform - allowing builds for Windows, Linux, and more. Unfortunately, attempting to build using cx_Freeze was resulting in errors: libpyside-python2.7.1.1.dylib: No such file or ... Continue reading

Pelicans on Webfaction  web

As mentioned in the previous post, I recently migrated this site over to the very clever Pelican. Setting it up was relatively straightforward using a combination of the official docs, this post and linked github repo from Dominic Rodger. That said, there were a few things that I stumbled at and non-obvious decisions that I’ve documented below. Continue reading

Speed up MATLAB on MacOS X  mac

On MacOS X 10.5 there is considerable slow-down in the MATLAB editor and other GUI elements. The issue is related to a change in the default Mac Java 2D rendering engine from Quartz2D (10.4) and Sun2D (10.5). This newer rendering engine improves performance for figure drawing, but ... Continue reading

Customize directory colors  bash

You can use the command ls —color (or an alias) to show directories with colours for folders, files, links, etc. However, you may not realise these colours can be easily configured using bashrc and a configuration file. Edit your .bashrc file (in your home directory) to include the following line ... Continue reading

Control memcached from the command line  bash

memcached is a general-purpose distributed memory caching system originally developed by Danga Interactive for LiveJournal but now used by many other sites. It is often used to speed up dynamic database-driven websites by caching data and objects in RAM to reduce the number of times an external data source (such ... Continue reading

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